100113 - Dr. B has set up some Help Session times for this week See the Google Calendar (link on left hand side of this page) for the times.
Location: wet lab (PAI 2.14)
Placing NADPH in your enzyme
Do this if your structure (x-ray or homology model) does not have the NADPH (or NADH) present
It should be there for when you are doing your virtual screening (just like when we had NADPH present when we docked against the DHF site of DHFR using MTX as the drug)
In General:
In PyMol: download your PDB
find another homologous structure in the PDB that has the NADPH present (e.g. your same enzyme in another organism)
load this into PyMol in the same session as your protein.
Delete any 'extra' chains on your protein or the homologous structure that you don't need (e.g. replicate chains)
Align the homologous structure to your structure (don't do the opposite - e.g. aligning yours to the homologous one. This would mess up your coordinates!)
See if the NADPH fits into a reasonable place on your protein (does it fit in a pocket)
-- if the molecule overlaps with atoms of your protein, then you can 'move' those atoms so that they are not.
-- change your mode in PyMol to '3-button editing', left click on an atom you want to move (it should have a gray sphere around it now), Ctrl+Shift+LeftClick on the atom to drag and move it out of the way of the protein atoms.
Move the NADPH to a new object
Delete the homologous protein (this should leave your NADPH in the PyMol window still)
Save the Protein + NADPH as a new, joined PDB file
Take this to ICM
-- you will use the NAPDH to define your docking site. However, you cannot just use the NADPH in this aligned position from PyMol because it might clash. So, you use ICM to redock it.
From PubChem, download the 3D SDF of NADPH
ICM will need to prep these ligands itself.
........
1st Task
Do homology model if you need to.
Homology Modeling:
if not in PDB, need to make homology model (see Bordoli 2009 Nature Protocols paper), see ICM website
Our VDS Homology Model protocol uploaded to GDocs/Protocols/VirtualScreening
ProtocolHomologyModelVDS_v4.doc
TIP: for a Homology model, you want to download the 'model' for virtual screening. Don't download the template file for screening.
093013 - an updated, full version is now posted on GDocs/Protocols/VirtualScreeningProtocols: ProtocolVirtualScreenYOURTarget_VDS_Fall13.doc
2nd Task
Finding a control set of ligands (need about 15 ligands - positive and negative)
all members of a Target team do this and compare results
3rd Task
run Lig Prep protocol on your ligands
all members of a Target team do this and compare results
4th Task
set up protein for docking
all members of a Target team do this and compare results
5th Task
run Control Ligands docking run
all members of a Target team do this and compare results
6th Task
run dockings against the Libraries
one member of the team will use GOLD other one will use ICM
NOTES - Dr. B 092513
Both people in a pair should independently screen cb306 and compare results - do you get the same thing in general?
Then split up and one person does GOLD screening for the other libraries and one person does ICM screening.
NOTE: if your jobs don't work - see the Tips & Hints page
2012 STUFF
VETERANS:
cb306 should be screened and examined ChembridgeDiversity should be started
and then, when that is done, also screen CB-kin_UT.sdf Optional: HF9PlatesPlates5_9.sdf - we have some of these in DMSO in the Robertus Lab Optional: InHouseCompounds (40 ligands) - we have these in DMSO in the VDS lab, supposedly.
SPRINGERS: You can go ahead and re-start your run for:cb306and then, when that is done, also screenCB-kin_UT.sdf
Do NOT screen anything big or it will get bogged down again and no one will get their screening finished.
The GOLD fitness function is made up of four components: • protein-ligand hydrogen bond energy (external H-bond)• protein-ligand van der Waals (vdw) energy (external vdw)• ligand internal vdw energy (internal vdw)• ligand torsional strain energy (internal torsion)• Optionally, a fifth component, ligand in tramolecular hydrogen bond energy (internal H-bond), may be added
The final ChemScore value is obtained by adding in a clash penalty and internal torsion terms,which militate against close contacts in docking and poor internal conformations. Covalent and constraint scores may also be included.
NOTE: for the concatenation scripts - use the ones in the /home/chem204/scripts folder instead of the one that is in the VirtualScreenRefresherFiles
-- these will allow you to append your Bestranking.lst and Output.sdf files correctly.
Blade Rules:
only run 1 job at a time
only use 6 processors per job
Everyone screens the HF9PlatesPlates5_9.sdf library first. Then, after the HF9 library, you want to screen the Chembridge libraries. Screen smallest to Largest.
cb-306 only has 306 ligands - so you can do it in one run.
AFTER these two runs - VERIFY that the ligands actually dock into the active site (open them up in PyMol with the protein). If they aren't in the right place, you will need to fix something.
Libraries Available (see further below for which ones you will screen).
CHEMBRIDGE
-rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf
-rw-r--r-- 1 beckham users 7.1M Jan 19 2010 Fragment-set_3D.sdf
-rw-r--r-- 1 beckham users 18M May 6 2009 CB-kin_UT.sdf
-rw-r--r-- 1 beckham users 29M Feb 18 2010 ION_Channel3D.sdf
-rw-r--r-- 1 beckham users 59M Feb 22 2010 KINASet3d.sdf
-rw-r--r-- 1 beckham users 69M Jan 19 2010 MW-set_3D.sdf
-rw-r--r-- 1 beckham users 134M Jan 19 2010 ChemBridge-diversity3D.sdf
-rw-r--r-- 1 beckham users 259M Feb 24 2010 CNS-Set3d.sdf
-rw-r--r-- 1 beckham users 860M Feb 22 2010 MicroFormats3D.sdf
MAYBRIDGE
-rw-r--r-- 1 beckham users 1.8M May 15 2009 HF9PlatesPlates5_9.sdf
-rw-r--r-- 1 beckham users 62M May 15 2009 HF9_180_Plates_1um3D_catnum.sdf
-rw-r--r-- 1 beckham users 174M May 6 2009 MayBridge50k_3D.sdf
SIGMA
-rw-r--r-- 1 beckham users 2.5M Sep 13 2009 zincSigmaLibrary3D.sdf
-rw-r--r-- 1 beckham users 3.5M Feb 26 2010 conformersLOPAC_3d.sdf
-rw-r--r-- 1 beckham users 6.1M Oct 14 2009 LOPAC_3d.sdf
NIH
-rw-r--r-- 1 beckham users 1.9M May 6 2009 NIH_ClinCol3Ded.sdf
MAYBRIDGE
-rw-r--r-- 1 beckham users 62M May 15 2009 HF9_180_Plates_1um3D_catnum.sdf (wait on this one)
Ling
CHEMBRIDGE
-rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf
-rw-r--r-- 1 beckham users 18M May 6 2009 CB-kin_UT.sdf
MAYBRIDGE
-rw-r--r-- 1 beckham users 174M May 6 2009 MayBridge50k_3D.sdf
Rishi
CHEMBRIDGE
-rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf
-rw-r--r-- 1 beckham users 18M May 6 2009 CB-kin_UT.sdf
Wolbachia endosymbiont of Brugia malayi Target - 1-deoxy-D-xylulose 5-phosphate reductoisomerase [DXR] (Wolbachia) Urvashi
CHEMBRIDGE
-rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf
-rw-r--r-- 1 beckham users 7.1M Jan 19 2010 Fragment-set_3D.sdf
-rw-r--r-- 1 beckham users 134M Jan 19 2010 ChemBridge-diversity3D.sdf
MAYBRIDGE
-rw-r--r-- 1 beckham users 62M May 15 2009 HF9_180_Plates_1um3D_catnum.sdf (wait on this one)
NIH
-rw-r--r-- 1 beckham users 1.9M May 6 2009 NIH_ClinCol3Ded.sdf (wait on this one)
Daniel - for DXR
MAYBRIDGE
-rw-r--r-- 1 beckham users 174M May 6 2009 MayBridge50k_3D.sdf
Target - FabI enoyl-acyl-carrier-protein reductase NADH (Wolbachia) Daniel - for FabI
CHEMBRIDGE
-rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf
-rw-r--r-- 1 beckham users 7.1M Jan 19 2010 Fragment-set_3D.sdf
-rw-r--r-- 1 beckham users 134M Jan 19 2010 ChemBridge-diversity3D.sdf
MAYBRIDGE
-rw-r--r-- 1 beckham users 62M May 15 2009 HF9_180_Plates_1um3D_catnum.sdf
NIH
-rw-r--r-- 1 beckham users 1.9M May 6 2009 NIH_ClinCol3Ded.sdf
Yersinia Target - Fab V (Yersinia Pestis) Both screen 3ZU4 and 3ZU5 against your respective libraries Do the chembridge libraries first, Then compare your top results and see which compounds do the best. - make your TopLigands for Chembridge compunds
We will worry about Maybridge after looking at Chembridge results
Max
CHEMBRIDGE
-rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf
-rw-r--r-- 1 beckham users 7.1M Jan 19 2010 Fragment-set_3D.sdf
-rw-r--r-- 1 beckham users 69M Jan 19 2010 MW-set_3D.sdf
-rw-r--r-- 1 beckham users 134M Jan 19 2010 ChemBridge-diversity3D.sdf
MAYBRIDGE
-rw-r--r-- 1 beckham users 1.8M May 15 2009 HF9PlatesPlates5_9.sdf (wait on this one)
-rw-r--r-- 1 beckham users 62M May 15 2009 HF9_180_Plates_1um3D_catnum.sdf (wait on this one)
NIH
-rw-r--r-- 1 beckham users 1.9M May 6 2009 NIH_ClinCol3Ded.sdf (wait on this one)
Michael
CHEMBRIDGE
-rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf
-rw-r--r-- 1 beckham users 259M Feb 24 2010 CNS-Set3d.sdf
-rw-r--r-- 1 beckham users 860M Feb 22 2010 MicroFormats3D.sdf
MAYBRIDGE
-rw-r--r-- 1 beckham users 174M May 6 2009 MayBridge50k_3D.sdf (wait on this one)
SIGMA
-rw-r--r-- 1 beckham users 2.5M Sep 13 2009 zincSigmaLibrary3D.sdf (wait on this one)
Virtual Screening Info:
Spring 2018
Directory is called "LabVS_ZincCBsplitLibrary", NOT "LabVS_CBsplitLibrary"
PUTTY no workey?
Use - PUTTY that can be run from the Desktop
putty.exe
(site for this file: http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html (Links to an external site.)
Download and run it from the desktop
Link to Chemical 3-D Minimization Resource
http://openbabel.org/wiki/Main_Page
NOTE: see Tips&Hints page for some other stuff on help with virtual
Are your top hits a PAIN?
http://www.nature.com/news/chemistry-chemical-con-artists-foil-drug-discovery-1.15991?WT.mc_id=TWT_NatureNews
Synopsis of Virtual Techniques (ligand based, structure based)
http://www.dddmag.com/articles/2013/12/new-approaches-virtual-screening
How promiscuous are your top hits?
http://chemutils.florida.scripps.edu:8080/pcpromiscuity/pcpromiscuity.html
Interesting Virtual Screening papers
BCR-ABL - uses MM-PBSA and Docking and MD simulationshttp://www.nature.com/srep/2014/141110/srep06948/full/srep06948.html
Docking Flow
Center for Structural Genomics of Infectious Diseases (CSGID)
http://link.springer.com/protocol/10.1007/978-1-4939-0354-2_19
Infectious Disease Virtual Screening slide deck
Overview of Virtual Steps
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3644978/
Commonly Screened Chemcal Databases (Cheng et al 2012)
*ARCHIVE**
Virtual Screening info:
2017 Stuff
LigPlot to show what your ligand looks like when docked (in 2-D)
European PDB info (EMBL-EBI)
http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=1u72&template=ligands.html&l=1.1
Spring 2017
Kelly - DONE
PUTTY no workey?
Use - PUTTY that can be run from the Desktop
putty.exe
(site for this file: http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html (Links to an external site.)
Download and run it from the desktop
Link to Chemical 3-D Minimization Resource
http://openbabel.org/wiki/Main_Page
NOTE: see Tips&Hints page for some other stuff on help with virtual
Are your top hits a PAIN?
http://www.nature.com/news/chemistry-chemical-con-artists-foil-drug-discovery-1.15991?WT.mc_id=TWT_NatureNews
Synopsis of Virtual Techniques (ligand based, structure based)
http://www.dddmag.com/articles/2013/12/new-approaches-virtual-screening
How promiscuous are your top hits?
http://chemutils.florida.scripps.edu:8080/pcpromiscuity/pcpromiscuity.html
Interesting Virtual Screening papers
BCR-ABL - uses MM-PBSA and Docking and MD simulationshttp://www.nature.com/srep/2014/141110/srep06948/full/srep06948.html
Docking Flow
Center for Structural Genomics of Infectious Diseases (CSGID)
http://link.springer.com/protocol/10.1007/978-1-4939-0354-2_19
Infectious Disease Virtual Screening slide deck
Overview of Virtual Steps
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3644978/
Commonly Screened Chemcal Databases (Cheng et al 2012)
Spring 2016
2013 Stuff
100113 - Dr. B has set up some Help Session times for this week See the Google Calendar (link on left hand side of this page) for the times.
Location: wet lab (PAI 2.14)
Placing NADPH in your enzyme
Do this if your structure (x-ray or homology model) does not have the NADPH (or NADH) presentIt should be there for when you are doing your virtual screening (just like when we had NADPH present when we docked against the DHF site of DHFR using MTX as the drug)
In General:
In PyMol: download your PDB
find another homologous structure in the PDB that has the NADPH present (e.g. your same enzyme in another organism)
load this into PyMol in the same session as your protein.
Delete any 'extra' chains on your protein or the homologous structure that you don't need (e.g. replicate chains)
Align the homologous structure to your structure (don't do the opposite - e.g. aligning yours to the homologous one. This would mess up your coordinates!)
See if the NADPH fits into a reasonable place on your protein (does it fit in a pocket)
-- if the molecule overlaps with atoms of your protein, then you can 'move' those atoms so that they are not.
-- change your mode in PyMol to '3-button editing', left click on an atom you want to move (it should have a gray sphere around it now), Ctrl+Shift+LeftClick on the atom to drag and move it out of the way of the protein atoms.
Move the NADPH to a new object
Delete the homologous protein (this should leave your NADPH in the PyMol window still)
Save the Protein + NADPH as a new, joined PDB file
Take this to ICM
-- you will use the NAPDH to define your docking site. However, you cannot just use the NADPH in this aligned position from PyMol because it might clash. So, you use ICM to redock it.
From PubChem, download the 3D SDF of NADPH
ICM will need to prep these ligands itself.
........
1st Task
Do homology model if you need to.Homology Modeling:
if not in PDB, need to make homology model (see Bordoli 2009 Nature Protocols paper), see ICM websiteOur VDS Homology Model protocol uploaded to GDocs/Protocols/VirtualScreening
ProtocolHomologyModelVDS_v4.doc
TIP: for a Homology model, you want to download the 'model' for virtual screening. Don't download the template file for screening.
093013 - an updated, full version is now posted on GDocs/Protocols/VirtualScreeningProtocols:
ProtocolVirtualScreenYOURTarget_VDS_Fall13.doc
2nd Task
Finding a control set of ligands (need about 15 ligands - positive and negative)all members of a Target team do this and compare results
3rd Task
run Lig Prep protocol on your ligandsall members of a Target team do this and compare results
4th Task
set up protein for dockingall members of a Target team do this and compare results
5th Task
run Control Ligands docking runall members of a Target team do this and compare results
6th Task
run dockings against the Librariesone member of the team will use GOLD other one will use ICM
NOTES - Dr. B 092513
Both people in a pair should independently screen cb306 and compare results - do you get the same thing in general?
Then split up and one person does GOLD screening for the other libraries and one person does ICM screening.
NOTE: if your jobs don't work - see the Tips & Hints page
2012 STUFF
VETERANS:cb306 should be screened and examined
ChembridgeDiversity should be started
and then, when that is done, also screen
CB-kin_UT.sdf
Optional: HF9PlatesPlates5_9.sdf - we have some of these in DMSO in the Robertus Lab
Optional: InHouseCompounds (40 ligands) - we have these in DMSO in the VDS lab, supposedly.
SPRINGERS:
You can go ahead and re-start your run for:cb306and then, when that is done, also screenCB-kin_UT.sdf
Do NOT screen anything big or it will get bogged down again and no one will get their screening finished.
101512
NOTE: the new version of GOLD (ver. 5.1) uses a new scoring system (PLP). The values of scores is different than what you would have gotten back in the Spring with GOLD Fitness score.
http://beta-www.ccdc.cam.ac.uk/Lists/DocumentationList/gold_release_notes.pdf
From GOLD User Guide v 5.2
The GOLD fitness function is made up of four components:
• protein-ligand hydrogen bond energy (external H-bond)• protein-ligand van der Waals (vdw) energy (external vdw)• ligand internal vdw energy (internal vdw)• ligand torsional strain energy (internal torsion)• Optionally, a fifth component, ligand in tramolecular hydrogen bond energy (internal H-bond), may be added
The final ChemScore value is obtained by adding in a clash penalty and internal torsion terms,which militate against close contacts in docking and poor internal conformations. Covalent and constraint scores may also be included.
Explanation of GOLD vs. Glide (from Penyu Ren lab at UT engineering)
http://biomol.bme.utexas.edu/wiki/index.php/ABS:Flexible_Docking_with_GOLD_and_GLIDE
Explanation of MM/PBS (from Pengyu Ren lab at UT engineering)
http://biomol.bme.utexas.edu/wiki/index.php/ABS:MM/PBSA_with_amber:_theory_and_application
NOTE: for the concatenation scripts - use the ones in the /home/chem204/scripts folder instead of the one that is in the VirtualScreenRefresherFiles
-- these will allow you to append your Bestranking.lst and Output.sdf files correctly.
Blade Rules:
Everyone screens the HF9PlatesPlates5_9.sdf library first. Then, after the HF9 library, you want to screen the Chembridge libraries. Screen smallest to Largest.
AFTER these two runs - VERIFY that the ligands actually dock into the active site (open them up in PyMol with the protein). If they aren't in the right place, you will need to fix something.
Libraries Available (see further below for which ones you will screen).
CHEMBRIDGE-rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf
-rw-r--r-- 1 beckham users 7.1M Jan 19 2010 Fragment-set_3D.sdf
-rw-r--r-- 1 beckham users 18M May 6 2009 CB-kin_UT.sdf
-rw-r--r-- 1 beckham users 29M Feb 18 2010 ION_Channel3D.sdf
-rw-r--r-- 1 beckham users 59M Feb 22 2010 KINASet3d.sdf
-rw-r--r-- 1 beckham users 69M Jan 19 2010 MW-set_3D.sdf
-rw-r--r-- 1 beckham users 134M Jan 19 2010 ChemBridge-diversity3D.sdf
-rw-r--r-- 1 beckham users 259M Feb 24 2010 CNS-Set3d.sdf
-rw-r--r-- 1 beckham users 860M Feb 22 2010 MicroFormats3D.sdf
MAYBRIDGE
-rw-r--r-- 1 beckham users 1.8M May 15 2009 HF9PlatesPlates5_9.sdf
-rw-r--r-- 1 beckham users 62M May 15 2009 HF9_180_Plates_1um3D_catnum.sdf
-rw-r--r-- 1 beckham users 174M May 6 2009 MayBridge50k_3D.sdf
SIGMA
-rw-r--r-- 1 beckham users 2.5M Sep 13 2009 zincSigmaLibrary3D.sdf
-rw-r--r-- 1 beckham users 3.5M Feb 26 2010 conformersLOPAC_3d.sdf
-rw-r--r-- 1 beckham users 6.1M Oct 14 2009 LOPAC_3d.sdf
NIH
-rw-r--r-- 1 beckham users 1.9M May 6 2009 NIH_ClinCol3Ded.sdf
2012 Targets
LeishmaniaTarget-serine-threonine protein phosphatase (Leishmania major)
Paul
CHEMBRIDGE
-rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf
-rw-r--r-- 1 beckham users 18M May 6 2009 CB-kin_UT.sdf
MAYBRIDGE
-rw-r--r-- 1 beckham users 62M May 15 2009 HF9_180_Plates_1um3D_catnum.sdf (wait on this one)
Ling
CHEMBRIDGE
-rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf
-rw-r--r-- 1 beckham users 18M May 6 2009 CB-kin_UT.sdf
MAYBRIDGE
-rw-r--r-- 1 beckham users 174M May 6 2009 MayBridge50k_3D.sdf
Rishi
CHEMBRIDGE
-rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf
-rw-r--r-- 1 beckham users 18M May 6 2009 CB-kin_UT.sdf
Wolbachia endosymbiont of Brugia malayi
Target - 1-deoxy-D-xylulose 5-phosphate reductoisomerase [DXR] (Wolbachia)
Urvashi
CHEMBRIDGE
-rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf
-rw-r--r-- 1 beckham users 7.1M Jan 19 2010 Fragment-set_3D.sdf
-rw-r--r-- 1 beckham users 134M Jan 19 2010 ChemBridge-diversity3D.sdf
MAYBRIDGE
-rw-r--r-- 1 beckham users 62M May 15 2009 HF9_180_Plates_1um3D_catnum.sdf (wait on this one)
NIH
-rw-r--r-- 1 beckham users 1.9M May 6 2009 NIH_ClinCol3Ded.sdf (wait on this one)
Daniel - for DXR
MAYBRIDGE
-rw-r--r-- 1 beckham users 174M May 6 2009 MayBridge50k_3D.sdf
Target - FabI enoyl-acyl-carrier-protein reductase NADH (Wolbachia)
Daniel - for FabI
CHEMBRIDGE
-rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf
-rw-r--r-- 1 beckham users 7.1M Jan 19 2010 Fragment-set_3D.sdf
-rw-r--r-- 1 beckham users 134M Jan 19 2010 ChemBridge-diversity3D.sdf
MAYBRIDGE
-rw-r--r-- 1 beckham users 62M May 15 2009 HF9_180_Plates_1um3D_catnum.sdf
NIH
-rw-r--r-- 1 beckham users 1.9M May 6 2009 NIH_ClinCol3Ded.sdf
Yersinia
Target - Fab V (Yersinia Pestis)
Both screen 3ZU4 and 3ZU5 against your respective libraries
Do the chembridge libraries first,
Then compare your top results and see which compounds do the best.
- make your TopLigands for Chembridge compunds
We will worry about Maybridge after looking at Chembridge results
Max
CHEMBRIDGE
-rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf
-rw-r--r-- 1 beckham users 7.1M Jan 19 2010 Fragment-set_3D.sdf
-rw-r--r-- 1 beckham users 69M Jan 19 2010 MW-set_3D.sdf
-rw-r--r-- 1 beckham users 134M Jan 19 2010 ChemBridge-diversity3D.sdf
MAYBRIDGE
-rw-r--r-- 1 beckham users 1.8M May 15 2009 HF9PlatesPlates5_9.sdf (wait on this one)
-rw-r--r-- 1 beckham users 62M May 15 2009 HF9_180_Plates_1um3D_catnum.sdf (wait on this one)
NIH
-rw-r--r-- 1 beckham users 1.9M May 6 2009 NIH_ClinCol3Ded.sdf (wait on this one)
Michael
CHEMBRIDGE
-rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf
-rw-r--r-- 1 beckham users 259M Feb 24 2010 CNS-Set3d.sdf
-rw-r--r-- 1 beckham users 860M Feb 22 2010 MicroFormats3D.sdf
MAYBRIDGE
-rw-r--r-- 1 beckham users 174M May 6 2009 MayBridge50k_3D.sdf (wait on this one)
SIGMA
-rw-r--r-- 1 beckham users 2.5M Sep 13 2009 zincSigmaLibrary3D.sdf (wait on this one)
Target- Protein Tyrosine Phosphate (Yersinia Enterocolitica)
Ivy
CHEMBRIDGE
-rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf
-rw-r--r-- 1 beckham users 18M May 6 2009 CB-kin_UT.sdf
Stephanie
CHEMBRIDGE
-rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf
-rw-r--r-- 1 beckham users 18M May 6 2009 CB-kin_UT.sdf
Jennifer
CHEMBRIDGE
-rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf
-rw-r--r-- 1 beckham users 18M May 6 2009 CB-kin_UT.sdf
Francisella tularensis
Target -1-deoxy-D-xylulose 5-phosphate reductoisomerase (Francisella Tularensis)
Janice
CHEMBRIDGE
-rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf
-rw-r--r-- 1 beckham users 7.1M Jan 19 2010 Fragment-set_3D.sdf
-rw-r--r-- 1 beckham users 69M Jan 19 2010 MW-set_3D.sdf
-rw-r--r-- 1 beckham users 134M Jan 19 2010 ChemBridge-diversity3D.sdf
MAYBRIDGE
-rw-r--r-- 1 beckham users 1.8M May 15 2009 HF9PlatesPlates5_9.sdf (wait on this one)
-rw-r--r-- 1 beckham users 62M May 15 2009 HF9_180_Plates_1um3D_catnum.sdf (wait on this one)
NIH
-rw-r--r-- 1 beckham users 1.9M May 6 2009 NIH_ClinCol3Ded.sdf (wait on this one)
Aldo
CHEMBRIDGE
-rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf
-rw-r--r-- 1 beckham users 259M Feb 24 2010 CNS-Set3d.sdf (wait on this one)
-rw-r--r-- 1 beckham users 860M Feb 22 2010 MicroFormats3D.sdf (wait on this one)
MAYBRIDGE
-rw-r--r-- 1 beckham users 174M May 6 2009 MayBridge50k_3D.sdf
SIGMA
-rw-r--r-- 1 beckham users 2.5M Sep 13 2009 zincSigmaLibrary3D.sdf (wait on this one)
Trypanosoma brucei
Target- Protein Phosphatase 2B
Divya
CHEMBRIDGE
-rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf
-rw-r--r-- 1 beckham users 18M May 6 2009 CB-kin_UT.sdf
Tom
CHEMBRIDGE
-rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf
-rw-r--r-- 1 beckham users 18M May 6 2009 CB-kin_UT.sdf
Sajan
CHEMBRIDGE
-rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf
-rw-r--r-- 1 beckham users 18M May 6 2009 CB-kin_UT.sdf
Plasmodium falciparans
Target - 1-deoxy-D-xylulose-5-phosphate reductoisomerase (P. falciparum)
Kaarthik
CHEMBRIDGE
-rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf
-rw-r--r-- 1 beckham users 7.1M Jan 19 2010 Fragment-set_3D.sdf
-rw-r--r-- 1 beckham users 134M Jan 19 2010 ChemBridge-diversity3D.sdf
MAYBRIDGE
-rw-r--r-- 1 beckham users 62M May 15 2009 HF9_180_Plates_1um3D_catnum.sdf
NIH
-rw-r--r-- 1 beckham users 1.9M May 6 2009 NIH_ClinCol3Ded.sdf
Andrew
CHEMBRIDGE
-rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf
-rw-r--r-- 1 beckham users 7.1M Jan 19 2010 Fragment-set_3D.sdf
-rw-r--r-- 1 beckham users 69M Jan 19 2010 MW-set_3D.sdf
-rw-r--r-- 1 beckham users 134M Jan 19 2010 ChemBridge-diversity3D.sdf
MAYBRIDGE
-rw-r--r-- 1 beckham users 174M May 6 2009 MayBridge50k_3D.sdf
Alex
use VINA too
CHEMBRIDGE
-rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf
-rw-r--r-- 1 beckham users 7.1M Jan 19 2010 Fragment-set_3D.sdf
-rw-r--r-- 1 beckham users 69M Jan 19 2010 MW-set_3D.sdf
-rw-r--r-- 1 beckham users 134M Jan 19 2010 ChemBridge-diversity3D.sdf
MAYBRIDGE
-rw-r--r-- 1 beckham users 174M May 6 2009 MayBridge50k_3D.sdf
-rw-r--r-- 1 beckham users 1.9M May 6 2009 NIH_ClinCol3Ded.sdf
Staphylococcus agalactiae - Neonatal Septicemia
Target - S. agalactiae serine-threonine phosphatase STP1
Suman
CHEMBRIDGE
-rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf
-rw-r--r-- 1 beckham users 18M May 6 2009 CB-kin_UT.sdf
Brandon
CHEMBRIDGE
-rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf
-rw-r--r-- 1 beckham users 18M May 6 2009 CB-kin_UT.sdf
Ruifei
CHEMBRIDGE
-rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf
-rw-r--r-- 1 beckham users 18M May 6 2009 CB-kin_UT.sdf
Listeria monocytogenes
Target - Protein Tyrosine Phosphatase (Listeria monocytogenes)
Akhilesh
CHEMBRIDGE
-rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf
-rw-r--r-- 1 beckham users 18M May 6 2009 CB-kin_UT.sdf
Mihir
CHEMBRIDGE
-rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf
-rw-r--r-- 1 beckham users 18M May 6 2009 CB-kin_UT.sdf
Shane
CHEMBRIDGE
-rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf
-rw-r--r-- 1 beckham users 18M May 6 2009 CB-kin_UT.sdf
Candida albicans
Target - Methionine Synthase
Priya
CHEMBRIDGE
-rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf
-rw-r--r-- 1 beckham users 7.1M Jan 19 2010 Fragment-set_3D.sdf
-rw-r--r-- 1 beckham users 134M Jan 19 2010 ChemBridge-diversity3D.sdf
MAYBRIDGE
-rw-r--r-- 1 beckham users 62M May 15 2009 HF9_180_Plates_1um3D_catnum.sdf
NIH
-rw-r--r-- 1 beckham users 1.9M May 6 2009 NIH_ClinCol3Ded.sdf
DROPPED TARGETS:
Trypanosoma cruzi
Target - dihydrofolate reductase-thymidylate synthase (T. cruzi)
Alex - use VINA too
CHEMBRIDGE
-rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf
-rw-r--r-- 1 beckham users 7.1M Jan 19 2010 Fragment-set_3D.sdf
-rw-r--r-- 1 beckham users 69M Jan 19 2010 MW-set_3D.sdf
-rw-r--r-- 1 beckham users 134M Jan 19 2010 ChemBridge-diversity3D.sdf
MAYBRIDGE
-rw-r--r-- 1 beckham users 1.8M May 15 2009 HF9PlatesPlates5_9.sdf
-rw-r--r-- 1 beckham users 62M May 15 2009 HF9_180_Plates_1um3D_catnum.sdf
NIH
-rw-r--r-- 1 beckham users 1.9M May 6 2009 NIH_ClinCol3Ded.sdf
Ling
CHEMBRIDGE
-rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf
-rw-r--r-- 1 beckham users 259M Feb 24 2010 CNS-Set3d.sdf
-rw-r--r-- 1 beckham users 860M Feb 22 2010 MicroFormats3D.sdf
MAYBRIDGE
-rw-r--r-- 1 beckham users 174M May 6 2009 MayBridge50k_3D.sdf
SIGMA
-rw-r--r-- 1 beckham users 2.5M Sep 13 2009 zincSigmaLibrary3D.sdf
Target - Glyceraldehyde-3-phosphate dehydrogenase (T. cruzi)
Andrew
CHEMBRIDGE
-rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf
-rw-r--r-- 1 beckham users 7.1M Jan 19 2010 Fragment-set_3D.sdf
-rw-r--r-- 1 beckham users 69M Jan 19 2010 MW-set_3D.sdf
-rw-r--r-- 1 beckham users 134M Jan 19 2010 ChemBridge-diversity3D.sdf
MAYBRIDGE
-rw-r--r-- 1 beckham users 1.8M May 15 2009 HF9PlatesPlates5_9.sdf
-rw-r--r-- 1 beckham users 62M May 15 2009 HF9_180_Plates_1um3D_catnum.sdf
NIH
-rw-r--r-- 1 beckham users 1.9M May 6 2009 NIH_ClinCol3Ded.sdf
Rishi
CHEMBRIDGE
-rw-r--r-- 1 beckham users 916K Mar 8 2010 cb_306_3d.sdf
-rw-r--r-- 1 beckham users 259M Feb 24 2010 CNS-Set3d.sdf
MAYBRIDGE
-rw-r--r-- 1 beckham users 174M May 6 2009 MayBridge50k_3D.sdf
SIGMA
-rw-r--r-- 1 beckham users 2.5M Sep 13 2009 zincSigmaLibrary3D.sdf
VIrtual Screening OLD